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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaactgacttggaacaagtgcaaataataaaccaaagacacactaaatgagttagacaaaatgtcttgtgctttgtcatctaacattgtggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCAGTGAATCCTAAATATATACTGAGGAACTATCTCTGCCAGACTGCAATTG

Basic information

species Glycine max
transcript GLYMA20G39090.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39090.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g21600.1 (Oryza sativa), 3'ss of exon 7
-tcaactgacttggaacaagtgcaaataataaaccaaagacacacta-aatgagttagacaaaatgtcttgtgctttgtcatctaacattgtggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCAGTGAATCCTAAATATATACTGAGGAACTATCTCTGCCAGACTGCAATTG
 ||||     |      || | ||  |   | |  || ||||   |  || |||         |  || |     |  | || ||   || |  |  || || |   | | |||||  | ||||| || ||||||||     | ||| | || || ||||| || ||| | ||  |||||||||||||||||||||||||||
ttcaaacatttatagcgaactacagctttgaga--aacgacaagttgtaaagaggctatttggacatccttgatctaatgatatatttttttctttgtgaagTTGGTTTCAAGTGGCGTTCCTGACGAAGAAAGGAAAGCTGCCATGAACTCTGTTAATCCAAAGTATGTTCTTCGGAACTATCTCTGCCAGACTGCAATTG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|20814084|gb|BQ298562.1|BQ298562
EST:     AGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|15814395|gb|BI786670.1|BI786670
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|18730535|gb|BM525932.1|BM525932
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|7692656|gb|AW760757.1|AW760757
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|22928662|gb|BU545801.1|BU545801
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTGATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|23725338|gb|BU760621.1|BU760621
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|15287927|gb|BI471818.1|BI471818
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCCGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
EST: gi|17963094|gb|BM269847.1|BM269847
EST:     AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAG                         GTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA
genomic: AAGAGCGTAAGGAAGCATGGACCAGTTGGTTGAAAGCTTATATACATGAGgtacagttat ... ggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgagttagacaaaatgtcttgtgctttgtcatctaacattgtggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCAGTGAATCCTAAATATATACTGAGGAACTATCTCTGCCAGACTGCAATTG
                                 atctaac  putative branch site (score: 2)
           acaaaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaactgacttggaacaagtgcaaataataaaccaaagacacactaaatgagttagacaaaatgtcttgtgctttgtcatctaacattgtggtaatgcagGTCTCTACCAGTGGGATACCTGATGACGAAAGGAAGATCTCGATGGATTCAGTGAATCCTAAATATATACTGAGGAACTATCTCTGCCAGACTGCAATTG

- - -tgacttg
- - - - - - - -caagtgc
- - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - -gacacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - agacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgtg